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- PDB-6mjz: Cryo-EM structure of Human Parainfluenza Virus Type 3 (hPIV3) in ... -

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Basic information

Entry
Database: PDB / ID: 6mjz
TitleCryo-EM structure of Human Parainfluenza Virus Type 3 (hPIV3) in complex with antibody PIA174
Components
  • Fusion glycoprotein F0
  • PIA174 Fab Heavy chain
  • PIA174 Fab Light chain
KeywordsVIRAL PROTEIN/immune system / hPIV3 Envelope / asymmetric / complex / antibody / VIRAL PROTEIN / VIRAL PROTEIN-immune system complex
Function / homologyFusion glycoprotein F0 / Precursor fusion glycoprotein F0, Paramyxoviridae / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / integral component of membrane / Fusion glycoprotein F0
Function and homology information
Specimen sourceHuman parainfluenza virus 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsAcharya, P. / Stewart-Jones, G. / Carragher, B. / Potter, C.S. / Kwong, P.D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure-based design of a quadrivalent fusion glycoprotein vaccine for human parainfluenza virus types 1-4.
Authors: Guillaume B E Stewart-Jones / Gwo-Yu Chuang / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Yaroslav Tsybovsky / Li Ou / Baoshan Zhang / Blanca Fernandez-Rodriguez / Valentina Gilardi / Chiara Silacci-Fregni / Martina Beltramello / Ulrich Baxa / Aliaksandr Druz / Wing-Pui Kong / Paul V Thomas / Yongping Yang / Kathryn E Foulds / John-Paul Todd / Hui Wei / Andres M Salazar / Diana G Scorpio / Bridget Carragher / Clinton S Potter / Davide Corti / John R Mascola / Antonio Lanzavecchia / Peter D Kwong
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 24, 2018 / Release: Nov 14, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 14, 2018Structure modelrepositoryInitial release
1.1Nov 28, 2018Structure modelData collection / Database referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Dec 12, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
H: PIA174 Fab Heavy chain
L: PIA174 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)211,1115
Polyers211,1115
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Fusion glycoprotein F0


Mass: 54970.625 Da / Num. of mol.: 3 / Source: (gene. exp.) Human parainfluenza virus 3 / Gene: F, KMQ_34898gpF / Production host: Homo sapiens (human) / References: UniProt: A0A059QA82
#2: Protein/peptide PIA174 Fab Heavy chain


Mass: 23512.453 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide PIA174 Fab Light chain


Mass: 22686.240 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of hPIV3 Env Q162C-L168C, I213C-G230C, A463V, I474Y in complex with antibody PIA174
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Human respirovirus 3
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.4 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4GctfCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 97177 / Symmetry type: POINT
Least-squares processHighest resolution: 4.3 Å

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